overhaul of pretty much everything

bobbypaton · Jun 28, 2022 · 0248a47 · 0248a47
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diff --git a/goodvibes/GoodVibes.py b/goodvibes/GoodVibes.py
diff --git a/goodvibes/examples/README b/goodvibes/examples/README
@@ -0,0 +1,4 @@
+* NO QH - turns off QH and also restricts printing columns
+* thermo has no parsing - move all to io
+* tidy methods in GV main script
+* sdf export
diff --git a/goodvibes/examples/gconf_ee_boltz/Aminoxylation_TS1_R.log b/goodvibes/examples/gconf_ee_boltz/Aminoxylation_TS1_R.log
diff --git a/goodvibes/examples/gconf_ee_boltz/Aminoxylation_TS2_S.log b/goodvibes/examples/gconf_ee_boltz/Aminoxylation_TS2_S.log
diff --git a/goodvibes/examples/gconf_ee_boltz/aminox_cat_conf212_S.log b/goodvibes/examples/gconf_ee_boltz/aminox_cat_conf212_S.log
diff --git a/goodvibes/examples/gconf_ee_boltz/aminox_cat_conf280_R.log b/goodvibes/examples/gconf_ee_boltz/aminox_cat_conf280_R.log
diff --git a/goodvibes/examples/gconf_ee_boltz/aminox_cat_conf65_S.log b/goodvibes/examples/gconf_ee_boltz/aminox_cat_conf65_S.log
diff --git a/goodvibes/examples/gconf_ee_boltz/aminox_subs_conf713.log b/goodvibes/examples/gconf_ee_boltz/aminox_subs_conf713.log
diff --git a/goodvibes/examples/gconf_ee_boltz/gconf_TS.yaml b/goodvibes/examples/gconf_ee_boltz/gconf_TS.yaml
diff --git a/goodvibes/examples/gconf_ee_boltz/gconf_aminox_cat.yaml b/goodvibes/examples/gconf_ee_boltz/gconf_aminox_cat.yaml
diff --git a/goodvibes/examples/reaction_profile/Int_III_Ph_a.log b/goodvibes/examples/reaction_profile/Int_III_Ph_a.log
diff --git a/goodvibes/examples/reaction_profile/Int_III_Ph_a_DLPNO.out b/goodvibes/examples/reaction_profile/Int_III_Ph_a_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_III_Py_a.log b/goodvibes/examples/reaction_profile/Int_III_Py_a.log
diff --git a/goodvibes/examples/reaction_profile/Int_III_Py_a_DLPNO.out b/goodvibes/examples/reaction_profile/Int_III_Py_a_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_III_Py_b.log b/goodvibes/examples/reaction_profile/Int_III_Py_b.log
diff --git a/goodvibes/examples/reaction_profile/Int_III_Py_b_DLPNO.out b/goodvibes/examples/reaction_profile/Int_III_Py_b_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_II_Ph_a.log b/goodvibes/examples/reaction_profile/Int_II_Ph_a.log
diff --git a/goodvibes/examples/reaction_profile/Int_II_Ph_a_DLPNO.out b/goodvibes/examples/reaction_profile/Int_II_Ph_a_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_II_Py_a.log b/goodvibes/examples/reaction_profile/Int_II_Py_a.log
diff --git a/goodvibes/examples/reaction_profile/Int_II_Py_a_DLPNO.out b/goodvibes/examples/reaction_profile/Int_II_Py_a_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_II_Py_b.log b/goodvibes/examples/reaction_profile/Int_II_Py_b.log
diff --git a/goodvibes/examples/reaction_profile/Int_II_Py_b_DLPNO.out b/goodvibes/examples/reaction_profile/Int_II_Py_b_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_II_Py_c.log b/goodvibes/examples/reaction_profile/Int_II_Py_c.log
diff --git a/goodvibes/examples/reaction_profile/Int_II_Py_c_DLPNO.out b/goodvibes/examples/reaction_profile/Int_II_Py_c_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Ph_a.log b/goodvibes/examples/reaction_profile/Int_I_Ph_a.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Ph_a_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Ph_a_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Ph_b.log b/goodvibes/examples/reaction_profile/Int_I_Ph_b.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Ph_b_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Ph_b_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Ph_c.log b/goodvibes/examples/reaction_profile/Int_I_Ph_c.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Ph_c_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Ph_c_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_a.log b/goodvibes/examples/reaction_profile/Int_I_Py_a.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_a_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Py_a_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_b.log b/goodvibes/examples/reaction_profile/Int_I_Py_b.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_b_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Py_b_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_c.log b/goodvibes/examples/reaction_profile/Int_I_Py_c.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_c_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Py_c_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_d.log b/goodvibes/examples/reaction_profile/Int_I_Py_d.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_d_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Py_d_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_e.log b/goodvibes/examples/reaction_profile/Int_I_Py_e.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_e_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Py_e_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_f.log b/goodvibes/examples/reaction_profile/Int_I_Py_f.log
diff --git a/goodvibes/examples/reaction_profile/Int_I_Py_f_DLPNO.out b/goodvibes/examples/reaction_profile/Int_I_Py_f_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/PhPy.yaml b/goodvibes/examples/reaction_profile/PhPy.yaml
@@ -0,0 +1,29 @@
+--- # PES
+    Ph: [Ph-Int1 + EtOH, Ph-TS1 + EtOH, Ph-Int2 + EtOH, Ph-TS2 + EtOH, Ph-Int3 + EtOH]
+    Py: [Py-Int1 + EtOH, Py-TS1 + EtOH, Py-Int2 + EtOH, Py-TS2 + EtOH, Py-Int3 + EtOH]
+
+--- # SPECIES
+    Ph-Int1     : Int_I_Ph*
+    Ph-TS1      : TS_1_Ph*
+    Ph-Int2     : Int_II_Ph*
+    Ph-TS2      : TS_II_Ph*
+    Ph-Int3     : Int_III_Ph*
+    Py-Int1     : Int_I_Py*
+    Py-TS1      : TS_1_Py*
+    Py-Int2     : Int_II_Py*
+    Py-TS2      : TS_II_Py*
+    Py-Int3     : Int_III_Py*
+    EtOH        : ethanol*
+
+--- # FORMAT
+    dec :  2 
+    legend : False
+    color : black,#26a6a4
+    pointlabel : False 
+    gridlines: True
+    show_conformers: True
+    show_gconf: False
+    dpi : 400
+    title: Potential Energy Surface
+
+
diff --git a/goodvibes/examples/reaction_profile/Rxn_profile_PhPy.png b/goodvibes/examples/reaction_profile/Rxn_profile_PhPy.png
diff --git a/goodvibes/examples/reaction_profile/TS_1_Ph_a.log b/goodvibes/examples/reaction_profile/TS_1_Ph_a.log
diff --git a/goodvibes/examples/reaction_profile/TS_1_Ph_a_DLPNO.out b/goodvibes/examples/reaction_profile/TS_1_Ph_a_DLPNO.out
diff --git a/goodvibes/examples/reaction_profile/TS_1_Ph_b.log b/goodvibes/examples/reaction_profile/TS_1_Ph_b.log
diff --git a/goodvibes/examples/reaction_profile/TS_1_Ph_b_DLPNO.out b/goodvibes/examples/reaction_profile/TS_1_Ph_b_DLPNO.out